Clashes through the night between police carrying riot shields and scores of demonstrators underscore the challenges China faces in Hong Kong as a restive younger generation challenges its influence in the former British colony.
Several people suffered minor injuries.
The protesters got into the city's main government compound late on Friday by forcing their way through a police cordon and scaling perimeter fences in the culmination of a week-long rally to demand free elections.
They were removed one by one, some of them carried away, according to witnesses. On Saturday, hundreds were still sitting near the compound close to Hong Kong's financial district.
"The police have used disproportionate force to stop the legitimate actions of the students and that should be condemned," said Benny Tai, one of the three main organizers of the pro-democracy Occupy Central movement.
Police arrested 61 people in the clearance operation, including 48 men and 13 women, Reuters reported.
Several thousand protesters had massed on streets outside the headquarters in the early hours of Saturday in support of those who had stormed inside, shouting "retreat, retreat, retreat" as police advanced and tried to stop them charging.
Many protesters used umbrellas to shield themselves from the pepper spray. Those who got hit used water to rinse their eyes.